SummaryAlpha shapes were invented in the early 80s of last century, and their implementation in three dimensions in the early 90s was at the forefront of the exact arithmetic paradigm that enabled fast and correct geometric software. In the late 90s, alpha shapes motivated the development of the wrap algorithm for surface reconstruction, and of persistent homology, which was the starting point of rapidly expanding interest in topological algorithms aimed at data analysis questions.
We now see alpha shapes, wrap complexes, and persistent homology as three aspects of a larger theory, which we propose to fully develop. This viewpoint was a long time coming and finds its clear expression within a generalized
version of discrete Morse theory. This unified framework offers new opportunities, including
(I) the adaptive reconstruction of shapes driven by the cavity structure;
(II) the stochastic analysis of all aspects of the theory;
(III) the computation of persistence of dense data, both in scale and in depth;
(IV) the study of long-range order in periodic and near-periodic point configurations.
These capabilities will significantly deepen as well as widen the theory and enable new applications in the sciences. To gain focus, we concentrate on low-dimensional applications in structural molecular biology and particle systems.

Alpha shapes were invented in the early 80s of last century, and their implementation in three dimensions in the early 90s was at the forefront of the exact arithmetic paradigm that enabled fast and correct geometric software. In the late 90s, alpha shapes motivated the development of the wrap algorithm for surface reconstruction, and of persistent homology, which was the starting point of rapidly expanding interest in topological algorithms aimed at data analysis questions.
We now see alpha shapes, wrap complexes, and persistent homology as three aspects of a larger theory, which we propose to fully develop. This viewpoint was a long time coming and finds its clear expression within a generalized
version of discrete Morse theory. This unified framework offers new opportunities, including
(I) the adaptive reconstruction of shapes driven by the cavity structure;
(II) the stochastic analysis of all aspects of the theory;
(III) the computation of persistence of dense data, both in scale and in depth;
(IV) the study of long-range order in periodic and near-periodic point configurations.
These capabilities will significantly deepen as well as widen the theory and enable new applications in the sciences. To gain focus, we concentrate on low-dimensional applications in structural molecular biology and particle systems.

Max ERC Funding

1 678 432 €

Duration

Start date: 2018-07-01, End date: 2023-06-30

Project acronymARCHADAPT

ProjectThe architecture of adaptation to novel environments

Researcher (PI)Christian Werner Schlötterer

Host Institution (HI)VETERINAERMEDIZINISCHE UNIVERSITAET WIEN

Call DetailsAdvanced Grant (AdG), LS8, ERC-2011-ADG_20110310

SummaryOne of the central goals in evolutionary biology is to understand adaptation. Experimental evolution represents a highly promising approach to study adaptation. In this proposal, a freshly collected D. simulans population will be allowed to adapt to laboratory conditions under two different temperature regimes: hot (27°C) and cold (18°C). The trajectories of adaptation to these novel environments will be monitored on three levels: 1) genomic, 2) transcriptomic, 3) phenotypic. Allele frequency changes during the experiment will be measured by next generation sequencing of DNA pools (Pool-Seq) to identify targets of selection. RNA-Seq will be used to trace adaptation on the transcriptomic level during three developmental stages. Eight different phenotypes will be scored to measure the phenotypic consequences of adaptation. Combining the adaptive trajectories on these three levels will provide a picture of adaptation for a multicellular, outcrossing organism that is far more detailed than any previous results.
Furthermore, the proposal addresses the question of how adaptation on these three levels is reversible if the environment reverts to ancestral conditions. The third aspect of adaptation covered in the proposal is the question of repeatability of adaptation. Again, this question will be addressed on the three levels: genomic, transcriptomic and phenotypic. Using replicates with different degrees of genetic similarity, as well as closely related species, we will test how similar the adaptive response is.
This large-scale study will provide new insights into the importance of standing variation for the adaptation to novel environments. Hence, apart from providing significant evolutionary insights on the trajectories of adaptation, the results we will obtain will have important implications for conservation genetics and commercial breeding.

One of the central goals in evolutionary biology is to understand adaptation. Experimental evolution represents a highly promising approach to study adaptation. In this proposal, a freshly collected D. simulans population will be allowed to adapt to laboratory conditions under two different temperature regimes: hot (27°C) and cold (18°C). The trajectories of adaptation to these novel environments will be monitored on three levels: 1) genomic, 2) transcriptomic, 3) phenotypic. Allele frequency changes during the experiment will be measured by next generation sequencing of DNA pools (Pool-Seq) to identify targets of selection. RNA-Seq will be used to trace adaptation on the transcriptomic level during three developmental stages. Eight different phenotypes will be scored to measure the phenotypic consequences of adaptation. Combining the adaptive trajectories on these three levels will provide a picture of adaptation for a multicellular, outcrossing organism that is far more detailed than any previous results.
Furthermore, the proposal addresses the question of how adaptation on these three levels is reversible if the environment reverts to ancestral conditions. The third aspect of adaptation covered in the proposal is the question of repeatability of adaptation. Again, this question will be addressed on the three levels: genomic, transcriptomic and phenotypic. Using replicates with different degrees of genetic similarity, as well as closely related species, we will test how similar the adaptive response is.
This large-scale study will provide new insights into the importance of standing variation for the adaptation to novel environments. Hence, apart from providing significant evolutionary insights on the trajectories of adaptation, the results we will obtain will have important implications for conservation genetics and commercial breeding.

SummaryI propose to study how eukaryotic cells generate autophagosomes, organelles bounded by a double membrane. These are formed during autophagy and mediate the degradation of cytoplasmic substances within the lysosomal compartment. Autophagy thereby protects the organism from pathological conditions such as neurodegeneration, cancer and infections. Many core factors required for autophagosome formation have been identified but the order in which they act and their mode of action is still unclear. We will use a combination of biochemical and cell biological approaches to elucidate the choreography and mechanism of these core factors. In particular, we will focus on selective autophagy and determine how the autophagic machinery generates an autophagosome that selectively contains the cargo.
To this end we will focus on the cytoplasm-to-vacuole-targeting pathway in S. cerevisiae that mediates the constitutive delivery of the prApe1 enzyme into the vacuole. We will use cargo mimetics or prApe1 complexes in combination with purified autophagy proteins and vesicles to reconstitute the process and so determine which factors are both necessary and sufficient for autophagosome formation, as well as elucidating their mechanism of action.
In parallel we will study selective autophagosome formation in human cells. This will reveal common principles and special adaptations. In particular, we will use cell lysates from genome-edited cells in combination with purified autophagy proteins to reconstitute selective autophagosome formation around ubiquitin-positive cargo material. The insights and hypotheses obtained from these reconstituted systems will be validated using cell biological approaches.
Taken together, our experiments will allow us to delineate the major steps of autophagosome formation during selective autophagy. Our results will yield detailed insights into how cells form and shape organelles in a de novo manner, which is major question in cell- and developmental biology.

I propose to study how eukaryotic cells generate autophagosomes, organelles bounded by a double membrane. These are formed during autophagy and mediate the degradation of cytoplasmic substances within the lysosomal compartment. Autophagy thereby protects the organism from pathological conditions such as neurodegeneration, cancer and infections. Many core factors required for autophagosome formation have been identified but the order in which they act and their mode of action is still unclear. We will use a combination of biochemical and cell biological approaches to elucidate the choreography and mechanism of these core factors. In particular, we will focus on selective autophagy and determine how the autophagic machinery generates an autophagosome that selectively contains the cargo.
To this end we will focus on the cytoplasm-to-vacuole-targeting pathway in S. cerevisiae that mediates the constitutive delivery of the prApe1 enzyme into the vacuole. We will use cargo mimetics or prApe1 complexes in combination with purified autophagy proteins and vesicles to reconstitute the process and so determine which factors are both necessary and sufficient for autophagosome formation, as well as elucidating their mechanism of action.
In parallel we will study selective autophagosome formation in human cells. This will reveal common principles and special adaptations. In particular, we will use cell lysates from genome-edited cells in combination with purified autophagy proteins to reconstitute selective autophagosome formation around ubiquitin-positive cargo material. The insights and hypotheses obtained from these reconstituted systems will be validated using cell biological approaches.
Taken together, our experiments will allow us to delineate the major steps of autophagosome formation during selective autophagy. Our results will yield detailed insights into how cells form and shape organelles in a de novo manner, which is major question in cell- and developmental biology.

Max ERC Funding

1 999 640 €

Duration

Start date: 2016-03-01, End date: 2021-02-28

Project acronymAuxinER

ProjectMechanisms of Auxin-dependent Signaling in the Endoplasmic Reticulum

Researcher (PI)Jürgen Kleine-Vehn

Host Institution (HI)UNIVERSITAET FUER BODENKULTUR WIEN

Call DetailsStarting Grant (StG), LS3, ERC-2014-STG

SummaryThe phytohormone auxin has profound importance for plant development. The extracellular AUXIN BINDING PROTEIN1 (ABP1) and the nuclear AUXIN F-BOX PROTEINs (TIR1/AFBs) auxin receptors perceive fast, non-genomic and slow, genomic auxin responses, respectively. Despite the fact that ABP1 mainly localizes to the endoplasmic reticulum (ER), until now it has been proposed to be active only in the extracellular matrix (reviewed in Sauer and Kleine-Vehn, 2011). Just recently, ABP1 function was also linked to genomic responses, modulating TIR1/AFB-dependent processes (Tromas et al., 2013). Intriguingly, the genomic effect of ABP1 appears to be at least partially independent of the endogenous auxin indole 3-acetic acid (IAA) (Paque et al., 2014).
In this proposal my main research objective is to unravel the importance of the ER for genomic auxin responses. The PIN-LIKES (PILS) putative carriers for auxinic compounds also localize to the ER and determine the cellular sensitivity to auxin. PILS5 gain-of-function reduces canonical auxin signaling (Barbez et al., 2012) and phenocopies abp1 knock down lines (Barbez et al., 2012, Paque et al., 2014). Accordingly, a PILS-dependent substrate could be a negative regulator of ABP1 function in the ER. Based on our unpublished data, an IAA metabolite could play a role in ABP1-dependent processes in the ER, possibly providing feedback on the canonical nuclear IAA-signaling.
I hypothesize that the genomic auxin response may be an integration of auxin- and auxin-metabolite-dependent nuclear and ER localized signaling, respectively. This proposed project aims to characterize a novel auxin-signaling paradigm in plants. We will employ state of the art interdisciplinary (biochemical, biophysical, computational modeling, molecular, and genetic) methods to assess the projected research. The identification of the proposed auxin conjugate-dependent signal could have far reaching plant developmental and biotechnological importance.

The phytohormone auxin has profound importance for plant development. The extracellular AUXIN BINDING PROTEIN1 (ABP1) and the nuclear AUXIN F-BOX PROTEINs (TIR1/AFBs) auxin receptors perceive fast, non-genomic and slow, genomic auxin responses, respectively. Despite the fact that ABP1 mainly localizes to the endoplasmic reticulum (ER), until now it has been proposed to be active only in the extracellular matrix (reviewed in Sauer and Kleine-Vehn, 2011). Just recently, ABP1 function was also linked to genomic responses, modulating TIR1/AFB-dependent processes (Tromas et al., 2013). Intriguingly, the genomic effect of ABP1 appears to be at least partially independent of the endogenous auxin indole 3-acetic acid (IAA) (Paque et al., 2014).
In this proposal my main research objective is to unravel the importance of the ER for genomic auxin responses. The PIN-LIKES (PILS) putative carriers for auxinic compounds also localize to the ER and determine the cellular sensitivity to auxin. PILS5 gain-of-function reduces canonical auxin signaling (Barbez et al., 2012) and phenocopies abp1 knock down lines (Barbez et al., 2012, Paque et al., 2014). Accordingly, a PILS-dependent substrate could be a negative regulator of ABP1 function in the ER. Based on our unpublished data, an IAA metabolite could play a role in ABP1-dependent processes in the ER, possibly providing feedback on the canonical nuclear IAA-signaling.
I hypothesize that the genomic auxin response may be an integration of auxin- and auxin-metabolite-dependent nuclear and ER localized signaling, respectively. This proposed project aims to characterize a novel auxin-signaling paradigm in plants. We will employ state of the art interdisciplinary (biochemical, biophysical, computational modeling, molecular, and genetic) methods to assess the projected research. The identification of the proposed auxin conjugate-dependent signal could have far reaching plant developmental and biotechnological importance.

SummaryComputational simulations of natural phenomena are essential in science, engineering, product design, architecture, and computer graphics applications. However, despite progress in numerical algorithms and computational power, it is still unfeasible to compute detailed simulations at large scales. To make matters worse, important phenomena like turbulent splashing liquids and fracturing solids rely on delicate coupling between small-scale details and large-scale behavior. Brute-force computation of such phenomena is intractable, and current adaptive techniques are too fragile, too costly, or too crude to capture subtle instabilities at small scales. Increases in computational power and parallel algorithms will improve the situation, but progress will only be incremental until we address the problem at its source.
I propose two main approaches to this problem of efficiently simulating large-scale liquid and solid dynamics. My first avenue of research combines numerics and shape: I will investigate a careful de-coupling of dynamics from geometry, allowing essential shape details to be preserved and retrieved without wasting computation. I will also develop methods for merging small-scale analytical solutions with large-scale numerical algorithms. (These ideas show particular promise for phenomena like splashing liquids and fracturing solids, whose small-scale behaviors are poorly captured by standard finite element methods.) My second main research direction is the manipulation of large-scale simulation data: Given the redundant and parallel nature of physics computation, we will drastically speed up computation with novel dimension reduction and data compression approaches. We can also minimize unnecessary computation by re-using existing simulation data. The novel approaches resulting from this work will undoubtedly synergize to enable the simulation and understanding of complicated natural and biological processes that are presently unfeasible to compute.

Computational simulations of natural phenomena are essential in science, engineering, product design, architecture, and computer graphics applications. However, despite progress in numerical algorithms and computational power, it is still unfeasible to compute detailed simulations at large scales. To make matters worse, important phenomena like turbulent splashing liquids and fracturing solids rely on delicate coupling between small-scale details and large-scale behavior. Brute-force computation of such phenomena is intractable, and current adaptive techniques are too fragile, too costly, or too crude to capture subtle instabilities at small scales. Increases in computational power and parallel algorithms will improve the situation, but progress will only be incremental until we address the problem at its source.
I propose two main approaches to this problem of efficiently simulating large-scale liquid and solid dynamics. My first avenue of research combines numerics and shape: I will investigate a careful de-coupling of dynamics from geometry, allowing essential shape details to be preserved and retrieved without wasting computation. I will also develop methods for merging small-scale analytical solutions with large-scale numerical algorithms. (These ideas show particular promise for phenomena like splashing liquids and fracturing solids, whose small-scale behaviors are poorly captured by standard finite element methods.) My second main research direction is the manipulation of large-scale simulation data: Given the redundant and parallel nature of physics computation, we will drastically speed up computation with novel dimension reduction and data compression approaches. We can also minimize unnecessary computation by re-using existing simulation data. The novel approaches resulting from this work will undoubtedly synergize to enable the simulation and understanding of complicated natural and biological processes that are presently unfeasible to compute.

Max ERC Funding

1 500 000 €

Duration

Start date: 2015-03-01, End date: 2020-02-29

Project acronymBrowsec

ProjectFoundations and Tools for Client-Side Web Security

Researcher (PI)Matteo MAFFEI

Host Institution (HI)TECHNISCHE UNIVERSITAET WIEN

Call DetailsConsolidator Grant (CoG), PE6, ERC-2017-COG

SummaryThe constantly increasing number of attacks on web applications shows how their rapid development has not been accompanied by adequate security foundations and demonstrates the lack of solid security enforcement tools. Indeed, web applications expose a gigantic attack surface, which hinders a rigorous understanding and enforcement of security properties. Hence, despite the worthwhile efforts to design secure web applications, users for a while will be confronted with vulnerable, or maliciously crafted, code. Unfortunately, end users have no way at present to reliably protect themselves from malicious applications.
BROWSEC will develop a holistic approach to client-side web security, laying its theoretical foundations and developing innovative security enforcement technologies. In particular, BROWSEC will deliver the first client-side tool to secure web applications that is practical, in that it is implemented as an extension and can thus be easily deployed at large, and also provably sound, i.e., backed up by machine-checked proofs that the tool provides end users with the required security guarantees. At the core of the proposal lies a novel monitoring technique, which treats the browser as a blackbox and intercepts its inputs and outputs in order to prevent dangerous information flows. With this lightweight monitoring approach, we aim at enforcing strong security properties without requiring any expensive and, given the dynamic nature of web applications, statically infeasible program analysis.
BROWSEC is thus a multidisciplinary research effort, promising practical impact and delivering breakthrough advancements in various disciplines, such as web security, JavaScript semantics, software engineering, and program verification.

The constantly increasing number of attacks on web applications shows how their rapid development has not been accompanied by adequate security foundations and demonstrates the lack of solid security enforcement tools. Indeed, web applications expose a gigantic attack surface, which hinders a rigorous understanding and enforcement of security properties. Hence, despite the worthwhile efforts to design secure web applications, users for a while will be confronted with vulnerable, or maliciously crafted, code. Unfortunately, end users have no way at present to reliably protect themselves from malicious applications.
BROWSEC will develop a holistic approach to client-side web security, laying its theoretical foundations and developing innovative security enforcement technologies. In particular, BROWSEC will deliver the first client-side tool to secure web applications that is practical, in that it is implemented as an extension and can thus be easily deployed at large, and also provably sound, i.e., backed up by machine-checked proofs that the tool provides end users with the required security guarantees. At the core of the proposal lies a novel monitoring technique, which treats the browser as a blackbox and intercepts its inputs and outputs in order to prevent dangerous information flows. With this lightweight monitoring approach, we aim at enforcing strong security properties without requiring any expensive and, given the dynamic nature of web applications, statically infeasible program analysis.
BROWSEC is thus a multidisciplinary research effort, promising practical impact and delivering breakthrough advancements in various disciplines, such as web security, JavaScript semantics, software engineering, and program verification.

Max ERC Funding

1 990 000 €

Duration

Start date: 2018-06-01, End date: 2023-05-31

Project acronymCDK6-DrugOpp

ProjectCDK6 in transcription - turning a foe in a friend

Researcher (PI)Veronika SEXL

Host Institution (HI)VETERINAERMEDIZINISCHE UNIVERSITAET WIEN

Call DetailsAdvanced Grant (AdG), LS7, ERC-2015-AdG

Summary"Translational research aims at applying mechanistic understanding in the development of "precision medicine", which depends on precise diagnostic tools and therapeutic approaches. Cancer therapy is experiencing a switch from non-specific, cytotoxic agents towards molecularly targeted and rationally designed compounds with the promise of greater efficacy and fewer side effects.
The two cell-cycle kinases CDK4 and CDK6 normally facilitate cell-cycle progression but are abnormally activated in certain cancers. CDK6 is up-regulated in hematopoietic malignancies, where it is the predominant cell-cycle kinase. The importance of CDK4/6 for tumor development is underscored by the fact that the US FDA selected inhibitors of the kinase activity of CDK4/6 as "breakthrough of the year 2013". Our recent findings suggest that the effects of the inhibitors may be limited as CDK6 is not only involved in cell-cycle progression: ground-breaking research in my group and others has shown that CDK6 is involved in regulation of transcription in a kinase-independent manner thereby driving the proliferation of leukemic stem cells and tumor formation. We have now identified mutations in CDK6 that convert it from a tumor promoter into a tumor suppressor. This unexpected outcome is accompanied by a distinct transcriptional profile. Separating the tumor-promoting from the tumor suppressive functions may open a novel therapeutic avenue for drug development. We aim at understanding which domains and residues of CDK6 are involved in rewiring the transcriptional landscape to pave the way for sophisticated inhibitors. The idea of turning a cancer cell's own most potent weapon against itself is novel and would represent a new paradigm for drug design. Finally, the understanding of CDK6 functions in tumor promotion and maintenance will also result in better patient stratification and improved treatment decisions for a broad spectrum of cancer types."

"Translational research aims at applying mechanistic understanding in the development of "precision medicine", which depends on precise diagnostic tools and therapeutic approaches. Cancer therapy is experiencing a switch from non-specific, cytotoxic agents towards molecularly targeted and rationally designed compounds with the promise of greater efficacy and fewer side effects.
The two cell-cycle kinases CDK4 and CDK6 normally facilitate cell-cycle progression but are abnormally activated in certain cancers. CDK6 is up-regulated in hematopoietic malignancies, where it is the predominant cell-cycle kinase. The importance of CDK4/6 for tumor development is underscored by the fact that the US FDA selected inhibitors of the kinase activity of CDK4/6 as "breakthrough of the year 2013". Our recent findings suggest that the effects of the inhibitors may be limited as CDK6 is not only involved in cell-cycle progression: ground-breaking research in my group and others has shown that CDK6 is involved in regulation of transcription in a kinase-independent manner thereby driving the proliferation of leukemic stem cells and tumor formation. We have now identified mutations in CDK6 that convert it from a tumor promoter into a tumor suppressor. This unexpected outcome is accompanied by a distinct transcriptional profile. Separating the tumor-promoting from the tumor suppressive functions may open a novel therapeutic avenue for drug development. We aim at understanding which domains and residues of CDK6 are involved in rewiring the transcriptional landscape to pave the way for sophisticated inhibitors. The idea of turning a cancer cell's own most potent weapon against itself is novel and would represent a new paradigm for drug design. Finally, the understanding of CDK6 functions in tumor promotion and maintenance will also result in better patient stratification and improved treatment decisions for a broad spectrum of cancer types."

SummaryEach year millions of animals undertake remarkable migratory journeys, across oceans and through hemispheres, guided by the Earth’s magnetic field. The cellular and molecular basis of this enigmatic sense, known as magnetoreception, remains an unsolved scientific mystery. One hypothesis that attempts to explain the basis of this sensory faculty is known as the magnetite theory of magnetoreception. It argues that magnetic information is transduced into a neuronal impulse by employing the iron oxide magnetite (Fe3O4). Current evidence indicates that pigeons employ a magnetoreceptor that is associated with the ophthalmic branch of the trigeminal nerve and the vestibular system, but the sensory cells remain undiscovered. The goal of this ambitious proposal is to discover the cells and molecules that mediate magnetoreception. This overall objective can be divided into three specific aims: (1) the identification of putative magnetoreceptive cells (PMCs); (2) the cellular characterisation of PMCs; and (3) the discovery and functional ablation of molecules specific to PMCs. In tackling these three aims this proposal adopts a reductionist mindset, employing and developing the latest imaging, subcellular, and molecular technologies.

Each year millions of animals undertake remarkable migratory journeys, across oceans and through hemispheres, guided by the Earth’s magnetic field. The cellular and molecular basis of this enigmatic sense, known as magnetoreception, remains an unsolved scientific mystery. One hypothesis that attempts to explain the basis of this sensory faculty is known as the magnetite theory of magnetoreception. It argues that magnetic information is transduced into a neuronal impulse by employing the iron oxide magnetite (Fe3O4). Current evidence indicates that pigeons employ a magnetoreceptor that is associated with the ophthalmic branch of the trigeminal nerve and the vestibular system, but the sensory cells remain undiscovered. The goal of this ambitious proposal is to discover the cells and molecules that mediate magnetoreception. This overall objective can be divided into three specific aims: (1) the identification of putative magnetoreceptive cells (PMCs); (2) the cellular characterisation of PMCs; and (3) the discovery and functional ablation of molecules specific to PMCs. In tackling these three aims this proposal adopts a reductionist mindset, employing and developing the latest imaging, subcellular, and molecular technologies.

Max ERC Funding

1 499 752 €

Duration

Start date: 2014-04-01, End date: 2019-03-31

Project acronymCharFL

ProjectCharacterizing the fitness landscape on population and global scales

Researcher (PI)Fyodor Kondrashov

Host Institution (HI)INSTITUTE OF SCIENCE AND TECHNOLOGYAUSTRIA

Call DetailsConsolidator Grant (CoG), LS2, ERC-2017-COG

SummaryThe fitness landscape, the representation of how the genotype manifests at the phenotypic (fitness) levels, may be among the most useful concepts in biology with impact on diverse fields, including quantitative genetics, emergence of pathogen resistance, synthetic biology and protein engineering. While progress in characterizing fitness landscapes has been made, three directions of research in the field remain virtually unexplored: the nature of the genotype to phenotype of standing variation (variation found in a natural population), the shape of the fitness landscape encompassing many genotypes and the modelling of complex genetic interactions in protein sequences.
The current proposal is designed to advance the study of fitness landscapes in these three directions using large-scale genomic experiments and experimental data from a model protein and theoretical work. The study of the fitness landscape of standing variation is aimed at the resolution of an outstanding question in quantitative genetics: the extent to which epistasis, non-additive genetic interactions, is shaping the phenotype. The second aim of characterizing the global fitness landscape will give us an understanding of how evolution proceeds along long evolutionary timescales, which can be directly applied to protein engineering and synthetic biology for the design of novel phenotypes. Finally, the third aim of modelling complex interactions will improve our ability to predict phenotypes from genotypes, such as the prediction of human disease mutations. In summary, the proposed study presents an opportunity to provide a unifying understanding of how phenotypes are shaped through genetic interactions. The consolidation of our empirical and theoretical work on different scales of the genotype to phenotype relationship will provide empirical data and novel context for several fields of biology.

The fitness landscape, the representation of how the genotype manifests at the phenotypic (fitness) levels, may be among the most useful concepts in biology with impact on diverse fields, including quantitative genetics, emergence of pathogen resistance, synthetic biology and protein engineering. While progress in characterizing fitness landscapes has been made, three directions of research in the field remain virtually unexplored: the nature of the genotype to phenotype of standing variation (variation found in a natural population), the shape of the fitness landscape encompassing many genotypes and the modelling of complex genetic interactions in protein sequences.
The current proposal is designed to advance the study of fitness landscapes in these three directions using large-scale genomic experiments and experimental data from a model protein and theoretical work. The study of the fitness landscape of standing variation is aimed at the resolution of an outstanding question in quantitative genetics: the extent to which epistasis, non-additive genetic interactions, is shaping the phenotype. The second aim of characterizing the global fitness landscape will give us an understanding of how evolution proceeds along long evolutionary timescales, which can be directly applied to protein engineering and synthetic biology for the design of novel phenotypes. Finally, the third aim of modelling complex interactions will improve our ability to predict phenotypes from genotypes, such as the prediction of human disease mutations. In summary, the proposed study presents an opportunity to provide a unifying understanding of how phenotypes are shaped through genetic interactions. The consolidation of our empirical and theoretical work on different scales of the genotype to phenotype relationship will provide empirical data and novel context for several fields of biology.

SummaryEpigenetics research has revealed that in the cell’s nucleus all kinds of biomolecules–DNA, RNAs, proteins, protein posttranslational modifications–are highly compartmentalized to occupy distinct chromatin territories and genomic loci, thereby contributing to gene regulation and cell identity. In contrast, small molecules and cellular metabolites are generally considered to passively enter the nucleus from the cytoplasm and to lack distinct subnuclear localization. The CHROMABOLISM proposal challenges this assumption based on preliminary data generated in my laboratory. I hypothesize that chromatin-bound enzymes of central metabolism and subnuclear metabolite gradients contribute to gene regulation and cellular identity.
To address this hypothesis, we will first systematically profile chromatin-bound metabolic enzymes, chart nuclear metabolomes across representative leukemia cell lines, and develop tools to measure local metabolite concentrations at distinct genomic loci. In a second step, we will then develop and apply technology to perturb these nuclear metabolite patterns by forcing the export of metabolic enzymes for the nucleus, aberrantly recruiting these enzymes to selected genomic loci, and perturbing metabolite patterns by addition and depletion of metabolites. In all these conditions we will measure the impact of nuclear metabolism on chromatin structure and gene expression. Based on the data obtained, we will model for the effects of cellular metabolites on cancer cell identity and proliferation. In line with the recent discovery of oncometabolites and the clinical use of antimetabolites, we expect to predict chromatin-bound metabolic enzymes that can be exploited as druggable targets in oncology. In a final aim we will validate these targets in leukemia and develop chemical probes against them.
Successful completion of this project has the potential to transform our understanding of nuclear metabolism in control of gene expression and cellular identity.

Epigenetics research has revealed that in the cell’s nucleus all kinds of biomolecules–DNA, RNAs, proteins, protein posttranslational modifications–are highly compartmentalized to occupy distinct chromatin territories and genomic loci, thereby contributing to gene regulation and cell identity. In contrast, small molecules and cellular metabolites are generally considered to passively enter the nucleus from the cytoplasm and to lack distinct subnuclear localization. The CHROMABOLISM proposal challenges this assumption based on preliminary data generated in my laboratory. I hypothesize that chromatin-bound enzymes of central metabolism and subnuclear metabolite gradients contribute to gene regulation and cellular identity.
To address this hypothesis, we will first systematically profile chromatin-bound metabolic enzymes, chart nuclear metabolomes across representative leukemia cell lines, and develop tools to measure local metabolite concentrations at distinct genomic loci. In a second step, we will then develop and apply technology to perturb these nuclear metabolite patterns by forcing the export of metabolic enzymes for the nucleus, aberrantly recruiting these enzymes to selected genomic loci, and perturbing metabolite patterns by addition and depletion of metabolites. In all these conditions we will measure the impact of nuclear metabolism on chromatin structure and gene expression. Based on the data obtained, we will model for the effects of cellular metabolites on cancer cell identity and proliferation. In line with the recent discovery of oncometabolites and the clinical use of antimetabolites, we expect to predict chromatin-bound metabolic enzymes that can be exploited as druggable targets in oncology. In a final aim we will validate these targets in leukemia and develop chemical probes against them.
Successful completion of this project has the potential to transform our understanding of nuclear metabolism in control of gene expression and cellular identity.